Cygnus is the evil class!

You then have someone breaking through the time gate of the Past releasing Pink Bean into the world as well.

1. Who actually released Pink Bean into the past?
2. How did Empress Cygnus get possessed or turned to evil?
3. Who programmed the computers and androids of the future to attack Tokyo?

Remember Dr. De Lang also created Humanoid A as well but he tried to re-create himself as the Black Mage.

I think you misinterpretted some things.

It was a Black Mage supporter who, trying to resurrect the Black Mage, failed and brought pink bean instead. It was probably a black wings member.

Empress Cygnus was looking into the World Tree (aka the Center of Victoria Island) and was caught in a trap that the Black mage set up. She and the knights subsequently had their souls stolen and became puppets to the Black Mage. This could indicate that the World Tree will be the end game location. (If they ever decide to end Maplestory)

NeoTokyo is non cannon.
Can't say much about NeoCity since I've never really bothered to look into it any.

And you misunderstood the quest text for the Magatia quests. Some members of the Zenumist and Alcadno societies THOUGHT he was trying to be like the Black Mage. And DeLang said that he had discovered Magatia's secret (that it was built off of the Black Mage's earlier experiments). He decided to use the information he learned from studying the Black Mage's alchemy in order to become immortal to stay with his family forever. So he built an adroid body that he put his soul into while he destroyed his lab and all of the Black Mage's notes so that no one could use them ever again.